Update README and small fixes #130
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JoseEspinosa
requested changes
Jun 18, 2024
README.md
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| Each row represents a set of sequences (in this case the seatoxin and toxin protein families) to be processed. | ||
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| `id` is the name of the set of sequences. It can correspond to the protein family name or to an internal id. | ||
| Each row represents a set of sequences (in this case the seatoxin and toxin protein families) to be aligned. |
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I think that explaining what each column represents (even if they are optional) as before would be clearer for users
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I was following the rnaseq structure and in the main they keep it super minimal and specify the columns in usage and this is what i tried to do - i could copy it here from usage but then it is maybe a bit redundant? I added some overview on the columns here bt not as secific as usage - let me know aht you think!
conf/test_parameters.config
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| // Output directory | ||
| outdir = "./outdir/" |
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| // Output directory | |
| outdir = "./outdir/" |
conf/test_full.config
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| // Output directory | ||
| outdir = "./outdir/" |
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outdir has to be implicitly provided since this won't in aws for instance that is why it has become a mandatory parameter, please also remove it from test.config
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| // Output directory | |
| outdir = "./outdir/" |
| ``` | ||
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| ### Multiple runs of the same sample | ||
| Each row represents a set of sequences (in this case the seatoxin and toxin protein families) to be processed. |
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this is not generic? I mean the example is still for "seatoxin and toxin protein families"?
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or maybe I am missing something, before we have two examples and now only one, right?
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sisi it is for 2 families, like in the main readme, but now we go into details on what each column is etc
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| process MULTIQC { | |||
| label 'process_medium' | |||
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| conda 'bioconda::multiqc=1.22.1' | |||
| container "community.wave.seqera.io/library/pip_multiqc:2c2e276ad8997cc4" | |||
| conda 'bioconda::multiqc=1.22.2' | |||
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couldn't we use the modules implementation of multiqc?
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No because i have to pass specific inputs that the normal one does not take - same as in rnaseq local multiqc
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closes #85 |
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Update README, small fixes and fix tests
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).